Currently I'm using My Fitness Pal a lot for tracking calories. I'm not sure though if I'll keep using it once the 12 weeks is up. It is awesome though that the app is free - and it allows you to add any missing food (though all the 12 wbt recipes are generally in there already so its super easy if you only eat what's in the program :)). The iphone app also has barcode scanner functionality which is awesome!
However my favourite app is the Nike Running app.
It has a really bad rap in the app store - but I use it to track my runs. On completion you put where you ran (ie. what terrain), your mood, and it uses local weather information and time to store that against your run too.
Where it really becomes awesome is if you remember to ever visit the website. You'll see a replay of your run (showing your pace), and it tracks achievements and stuff. Here's a sample: